diff README.rst @ 3:d4111d1de76f draft default tip

v0.0.8, expose kodoja_VRL.tsv output

--- a/README.rst	Mon Sep 10 09:16:13 2018 -0400
+++ b/README.rst	Fri Sep 14 09:55:56 2018 -0400
@@ -54,17 +54,29 @@
     $ wget https://zenodo.org/record/1406071/files/kodojaDB_v1.0.tar.gz
     $ tar -zxvf kodojaDB_v1.0.tar.gz
 
-Then update your Galaxy configuration in ``tool-data/kraken_databases.loc``
-to add a line like this::
+Each installed version of Kodoja (or Kraken or Kaiju) will have its own
+``*.loc`` files, which Galaxy will merge into a single list. e.g.::
+
+    $ find /path/to/galaxy/tool-data -name kaiju_databases.loc
+    $ find /path/to/galaxy/tool-data -name kraken_databases.loc
+
+Edit a ``kraken_databases.loc`` file to add a line like this, where
+``(tab)`` represents inserting a tab character (NOT spaces)::
 
     kodojaDB_v1.0_kraken(tab)KodojaDB v1.0 (kraken), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/krakenDB
 
-And likewise update ``tool-data/kaiju_databases.loc`` with a line like::
+And likewise update ``kaiju_databases.loc`` with a line like::
 
     kodojaDB_v1.0_kaiju(tab)KodojaDB v1.0 (kaiju), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/kaijuDB
 
 At the time of writing, reloading the ``*.loc`` files required restarting
-the Galaxy server.
+the Galaxy server, or doing this explicitly via the "Data tables registry"
+available under Server Administration if logged into Galaxy as an administator.
+
+It is our personal preference to work with ``tool-data/kraken_databases.loc``
+and ``tool-data/kaiju_databases.loc``, but if these are being ignored, you
+*may* need to enable this by adding the XML data table entries from our file
+``tool_data_table_conf.xml.sample`` to ``config/tool_data_table_conf.xml``.
 
 
 History
@@ -80,6 +92,9 @@
 v0.0.7  - Minor update to call ``kodoja_search.py`` v0.0.6.
         - Update help text, including zeros in columns 6 and 7.
         - Support ``$GALAXY_SLOTS``, defaulting to using four threads.
+v0.0.8  - Minor update to call ``kodoja_search.py`` v0.0.8.
+        - Option to capture the ``kodoja_VRL.tsv`` read table.
+        - Accept ``kraken_databases.loc`` entry style for old Kraken wrapper.
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